81 research outputs found
Detailed simulations of cell biology with Smoldyn 2.1.
Most cellular processes depend on intracellular locations and random collisions of individual protein molecules. To model these processes, we developed algorithms to simulate the diffusion, membrane interactions, and reactions of individual molecules, and implemented these in the Smoldyn program. Compared to the popular MCell and ChemCell simulators, we found that Smoldyn was in many cases more accurate, more computationally efficient, and easier to use. Using Smoldyn, we modeled pheromone response system signaling among yeast cells of opposite mating type. This model showed that secreted Bar1 protease might help a cell identify the fittest mating partner by sharpening the pheromone concentration gradient. This model involved about 200,000 protein molecules, about 7000 cubic microns of volume, and about 75 minutes of simulated time; it took about 10 hours to run. Over the next several years, as faster computers become available, Smoldyn will allow researchers to model and explore systems the size of entire bacterial and smaller eukaryotic cells
On the Statistics of Reaction-Diffusion Simulations for Molecular Communication
A molecule traveling in a realistic propagation environment can experience
stochastic interactions with other molecules and the environment boundary. The
statistical behavior of some isolated phenomena, such as dilute unbounded
molecular diffusion, are well understood. However, the coupling of multiple
interactions can impede closed-form analysis, such that simulations are
required to determine the statistics. This paper compares the statistics of
molecular reaction-diffusion simulation models from the perspective of
molecular communication systems. Microscopic methods track the location and
state of every molecule, whereas mesoscopic methods partition the environment
into virtual containers that hold molecules. The properties of each model are
described and compared with a hybrid of both models. Simulation results also
assess the accuracy of Poisson and Gaussian approximations of the underlying
Binomial statistics.Comment: 6 pages, 1 table, 10 figures. Submitted to the 2nd ACM International
Conference on Nanoscale Computing and Communication (ACM NANOCOM 2015) on May
16, 201
Multi-Scale Stochastic Simulation for Diffusive Molecular Communication
Recently, hybrid models have emerged that combine microscopic and mesoscopic
regimes in a single stochastic reaction-diffusion simulation. Microscopic
simulations track every individual molecule and are generally more accurate.
Mesoscopic simulations partition the environment into subvolumes, track when
molecules move between adjacent subvolumes, and are generally more
computationally efficient. In this paper, we present the foundation of a
multi-scale stochastic simulator from the perspective of molecular
communication, for both mesoscopic and hybrid models, where we emphasize
simulation accuracy at the receiver and efficiency in regions that are far from
the communication link. Our multi-scale models use subvolumes of different
sizes, between which we derive the diffusion event transition rate. Simulation
results compare the accuracy and efficiency of traditional approaches with that
of a regular hybrid method and with those of our proposed multi-scale methods.Comment: 7 pages, 2 tables, 6 figures. Will be presented at the 2015 IEEE
International Conference on Communications (ICC) in June 201
Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions
A class of Brownian dynamics algorithms for stochastic reaction-diffusion
models which include reversible bimolecular reactions is presented and
analyzed. The method is a generalization of the --\newrho model for
irreversible bimolecular reactions which was introduced in [arXiv:0903.1298].
The formulae relating the experimentally measurable quantities (reaction rate
constants and diffusion constants) with the algorithm parameters are derived.
The probability of geminate recombination is also investigated.Comment: 16 pages, 13 figures, submitted to SIAM Appl Mat
On the Reaction Diffusion Master Equation in the Microscopic Limit
Stochastic modeling of reaction-diffusion kinetics has emerged as a powerful
theoretical tool in the study of biochemical reaction networks. Two frequently
employed models are the particle-tracking Smoluchowski framework and the
on-lattice Reaction-Diffusion Master Equation (RDME) framework. As the mesh
size goes from coarse to fine, the RDME initially becomes more accurate.
However, recent developments have shown that it will become increasingly
inaccurate compared to the Smoluchowski model as the lattice spacing becomes
very fine. In this paper we give a new, general and simple argument for why the
RDME breaks down. Our analysis reveals a hard limit on the voxel size for which
no local RDME can agree with the Smoluchowski model
The Two Regime method for optimizing stochastic reaction-diffusion simulations
The computer simulation of stochastic reaction-diffusion processes in biology is often done using either compartment-based (spatially discretized) simulations or molecular-based (Brownian dynamics) approaches. Compartment-based approaches can yield quick and accurate mesoscopic results but lack the level of detail that is characteristic of the more computationally intensive molecular-based models. Often microscopic detail is only required in a small region but currently the best way to achieve this detail is to use a resource intensive model over the whole domain. We introduce the Two Regime Method (TRM) in which a molecular-based algorithm is used in part of the computational domain and a compartment-based approach is used elsewhere in the computational domain. We apply the TRM to two test problems including a model from developmental biology. We thereby show that the TRM is accurate and subsequently may be used to inspect both mesoscopic and microscopic detail of reaction diffusion simulations according to the demands of the modeller
Analysis of Brownian dynamics simulations of reversible biomolecular reactions
A class of Brownian dynamics algorithms for stochastic reaction-diffusion models which include reversible bimolecular reactions is presented and analyzed. The method is a generalization of the λ-rho model for irreversible bimolecular reactions which was introduced in [11]. The formulae relating the experimentally measurable quantities (reaction rate constants and diffusion constants) with the algorithm parameters are derived. The probability of geminate recombination is also investigated
- …